Chad W. Farris

Guoyao Shen, Boran Hao, Mengyu Li et al.

The application of compressed sensing (CS)-enabled data reconstruction for accelerating magnetic resonance imaging (MRI) remains a challenging problem. This is due to the fact that the information lost in k-space from the acceleration mask makes it difficult to reconstruct an image similar to the quality of a fully sampled image. Multiple deep learning-based structures have been proposed for MRI reconstruction using CS, both in the k-space and image domains as well as using unrolled optimization methods. However, the drawback of these structures is that they are not fully utilizing the information from both domains (k-space and image). Herein, we propose a deep learning-based attention hybrid variational network that performs learning in both the k-space and image domain. We evaluate our method on a well-known open-source MRI dataset and a clinical MRI dataset of patients diagnosed with strokes from our institution to demonstrate the performance of our network. In addition to quantitative evaluation, we undertook a blinded comparison of image quality across networks performed by a subspecialty trained radiologist. Overall, we demonstrate that our network achieves a superior performance among others under multiple reconstruction tasks.

Guoyao Shen, Mengyu Li, Chad W. Farris et al.

Deep learning-based MRI reconstruction models have achieved superior performance these days. Most recently, diffusion models have shown remarkable performance in image generation, in-painting, super-resolution, image editing and more. As a generalized diffusion model, cold diffusion further broadens the scope and considers models built around arbitrary image transformations such as blurring, down-sampling, etc. In this paper, we propose a k-space cold diffusion model that performs image degradation and restoration in k-space without the need for Gaussian noise. We provide comparisons with multiple deep learning-based MRI reconstruction models and perform tests on a well-known large open-source MRI dataset. Our results show that this novel way of performing degradation can generate high-quality reconstruction images for accelerated MRI.

Guoyao Shen, Yancheng Zhu, Mengyu Li et al.

Recent advances in MRI reconstruction have demonstrated remarkable success through deep learning-based models. However, most existing methods rely heavily on large-scale, task-specific datasets, making reconstruction in data-limited settings a critical yet underexplored challenge. While regularization by denoising (RED) leverages denoisers as priors for reconstruction, we propose Regularization by Neural Style Transfer (RNST), a novel framework that integrates a neural style transfer (NST) engine with a denoiser to enable magnetic field-transfer reconstruction. RNST generates high-field-quality images from low-field inputs without requiring paired training data, leveraging style priors to address limited-data settings. Our experiment results demonstrate RNST's ability to reconstruct high-quality images across diverse anatomical planes (axial, coronal, sagittal) and noise levels, achieving superior clarity, contrast, and structural fidelity compared to lower-field references. Crucially, RNST maintains robustness even when style and content images lack exact alignment, broadening its applicability in clinical environments where precise reference matches are unavailable. By combining the strengths of NST and denoising, RNST offers a scalable, data-efficient solution for MRI field-transfer reconstruction, demonstrating significant potential for resource-limited settings.

Mengyu Li, Guoyao Shen, Chad W. Farris et al.

Machine learning using transformers has shown great potential in medical imaging, but its real-world applicability remains limited due to the scarcity of annotated data. In this study, we propose a practical framework for the few-shot deployment of pretrained MRI transformers in diverse brain imaging tasks. By utilizing the Masked Autoencoder (MAE) pretraining strategy on a large-scale, multi-cohort brain MRI dataset comprising over 31 million slices, we obtain highly transferable latent representations that generalize well across tasks and datasets. For high-level tasks such as classification, a frozen MAE encoder combined with a lightweight linear head achieves state-of-the-art accuracy in MRI sequence identification with minimal supervision. For low-level tasks such as segmentation, we propose MAE-FUnet, a hybrid architecture that fuses multiscale CNN features with pretrained MAE embeddings. This model consistently outperforms other strong baselines in both skull stripping and multi-class anatomical segmentation under data-limited conditions. With extensive quantitative and qualitative evaluations, our framework demonstrates efficiency, stability, and scalability, suggesting its suitability for low-resource clinical environments and broader neuroimaging applications.

Guoyao Shen, Mengyu Li, Stephan Anderson et al.

Recent advancements in deep learning have enabled the development of generalizable models that achieve state-of-the-art performance across various imaging tasks. Vision Transformer (ViT)-based architectures, in particular, have demonstrated strong feature extraction capabilities when pre-trained on large-scale datasets. In this work, we introduce the Magnetic Resonance Image Processing Transformer (MR-IPT), a ViT-based framework designed to enhance the generalizability and robustness of accelerated MRI reconstruction. Unlike conventional deep learning models that require separate training for different acceleration factors, MR-IPT is pre-trained on a large-scale dataset encompassing multiple undersampling patterns and acceleration settings, enabling a unified reconstruction framework. By leveraging a shared transformer backbone, MR-IPT effectively learns universal feature representations, allowing it to generalize across diverse reconstruction tasks. Extensive experiments demonstrate that MR-IPT outperforms both CNN-based and existing transformer-based methods, achieving superior reconstruction quality across varying acceleration factors and sampling masks. Moreover, MR-IPT exhibits strong robustness, maintaining high performance even under unseen acquisition setups, highlighting its potential as a scalable and efficient solution for accelerated MRI. Our findings suggest that transformer-based general models can significantly advance MRI reconstruction, offering improved adaptability and stability compared to traditional deep learning approaches.